Hi @glaucod, i also had your issue and would like to know your htaccess configuration so maybe i could fix this. Specifically, my subsite seems to behave well, i can access it and manage it, but when i hover the “my sites” button in the navigation dashboard it only shows my main site. So to access the subsite i need to go on manage network->sites.
This may seems a little problem but maybe it is hiding something bigger.